The invention relates to a method and a system applied to high-throughput integration calculation and data management of material gene engineering. The method comprises the following steps: acquiring a large quantity of initial structures; selecting a first principle calculation task; carrying out high-throughput screening on the initial structures to obtain a valid structure; recommending a calculation parameter according to the valid structure and the first principle calculation task; setting a calculation resource, generating a calculation resource configuration file and saving the calculation resource configuration file; submitting the valid structure, the calculation parameter and the calculation resource configuration file to a calculation cluster, calculating and monitoring, and automatically correcting errors; extracting or processing a calculation result file after the calculation is completed to obtain a calculation result and descriptor data, and saving the calculation result and the descriptor data in a first principle calculation database. Through the method and the system applied to high-throughput integration calculation and data management of material gene engineering, the high-throughput automatic-process first principle calculation is achieved; the data can be automatically extracted, processed and accessed, so that a user can conveniently carry out the automatic-process high-throughput first principle calculation.